Maize network analysis revealed gene modules involved in development, nutrients utilization, metabolism, and stress response.
Maize network analysis revealed gene modules involved in development, nutrients utilization, metabolism, and stress response.
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玉米网络分析揭示了参与发育、营养利用、代谢和应激反应的基因模块
DOI：
10.1186/s12870-017-1077-4
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发表时间：
2017-08-01
影响因子：
5.3
通讯作者：
Li P
中科院分区：
文献类型：
--
作者：
Ma S;Ding Z;Li P
背景生物学中大数据的出现为获得生物学见解提供了机遇，同时也带来了挑战。对于玉米，大量的公开可用的转录组数据集已经产生，但缺乏全面的analysis.ResultsWe构建了一个玉米基因共表达网络的基础上的图形高斯模型，使用大量的RNA-seq数据。该网络包含20，269个基因，组装成964个基因模块，这些基因模块在各种植物过程中发挥作用，例如细胞组织，花序，叶舌和内核的发育，营养物质（例如氮和磷酸盐）的吸收和利用，苯并恶嗪酮，氧脂，类黄酮和蜡的代谢以及对胁迫的反应。其中，花序发育模块富含控制植物结构和籽粒结构的驯化基因（likera 1，ba 1，gt 1，tb 1，tga 1），而多个其他模块与不同的农艺性状相关。包含在这些模块内的是转录因子，其作为相同模块内的基因的已知或潜在的表达调节剂，表明它们作为相关生物过程的候选调节剂。与已建立的拟南芥网络的比较揭示了涉及细胞组织、营养吸收和利用以及代谢的特定模块的保守基因关联模式。分析还确定了两个物种之间的显着分歧的模块，编排developmental pathways.ConclusionsThis网络揭示了基因模块是如何组织不同物种之间的进化分歧的背景下，并突出模块的结构和基因内容可以提供重要的资源，玉米基因功能的研究与应用潜力。
BackgroundThe advent of big data in biology offers opportunities while poses challenges to derive biological insights. For maize, a large amount of publicly available transcriptome datasets have been generated but a comprehensive analysis is lacking.ResultsWe constructed a maize gene co-expression network based on the graphical Gaussian model, using massive RNA-seq data. The network, containing 20,269 genes, assembles into 964 gene modules that function in a variety of plant processes, such as cell organization, the development of inflorescences, ligules and kernels, the uptake and utilization of nutrients (e.g. nitrogen and phosphate), the metabolism of benzoxazionids, oxylipins, flavonoids, and wax, and the response to stresses. Among them, the inflorescences development module is enriched with domestication genes (likera1,ba1,gt1,tb1,tga1) that control plant architecture and kernel structure, while multiple other modules relate to diverse agronomic traits. Contained within these modules are transcription factors acting as known or potential expression regulators for the genes within the same modules, suggesting them as candidate regulators for related biological processes. A comparison with an established Arabidopsis network revealed conserved gene association patterns for specific modules involved in cell organization, nutrients uptake & utilization, and metabolism. The analysis also identified significant divergences between the two species for modules that orchestrate developmental pathways.ConclusionsThis network sheds light on how gene modules are organized between different species in the context of evolutionary divergence and highlights modules whose structure and gene content can provide important resources for maize gene functional studies with application potential.
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影响因子：
14.9
作者：
Andorf CM;Cannon EK;Portwood JL 2nd;Gardiner JM;Harper LC;Schaeffer ML;Braun BL;Campbell DA;Vinnakota AG;Sribalusu VV;Huerta M;Cho KT;Wimalanathan K;Richter JD;Mauch ED;Rao BS;Birkett SM;Sen TZ;Lawrence-Dill CJ
通讯作者：
Lawrence-Dill CJ
影响因子：
8.8
作者：
Fertuzinhos S;Li M;Kawasawa YI;Ivic V;Franjic D;Singh D;Crair M;Sestan N
通讯作者：
Sestan N
影响因子：
3.7
作者：
Childs KL;Davidson RM;Buell CR
通讯作者：
Buell CR
影响因子：
64.8
作者：
Doebley, J;Stec, A;Hubbard, L
通讯作者：
Hubbard, L
影响因子：
11.6
作者：
Goodman, CD;Casati, P;Walbot, V
通讯作者：
Walbot, V